2Matrix: A utility for indel coding and phylogenetic matrix concatenation

Applications in Plant Sciences

Volumn 2, Issue 1, 2014, Pages

  Salinas, Nelson R ^a,b   Little, Damon P ^b  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b Cullman Program for Molecular Systematics   (United States)

Author keywords

2matrix; File conversion; Indel coding; Software

Indexed keywords

EID: 84915738810     PISSN: 21680450     EISSN: 15372197     Source Type: Journal    
DOI: 10.3732/apps.1300083     Document Type: Article

References (11)

1. DOYLE , J. A. , AND P. K. ENDRESS . 2000. Morphological phylogenetic analysis of basal angiosperms: Comparison and combination with molecular data. International Journal of Plant Sciences 161 : S121-S153 .
2. GOLOBOFF , P. A. , J. S. FARRIS , AND K. C. NIXON . 2008 . TNT, a free program for phylogenetic analysis. Cladistics 24 : 774-786 .
3. LEWIS , P. O. 2003 . NCL: A C++ class library for interpreting data f iles in NEXUS format. Bioinformatics (Oxford, England) 19 : 2330-2331 .
4. LITTLE , D. P. 2005 . 2xread: A simple indel coding tool. Available at: http://www.nybg.org/f iles/scientists/2xread.html [accessed 16 December 2013].
5. MADDISON , D. R. , D. L. SWOFFORD , AND W. P. MADDISON . 1997. NEXUS: An extensible f ile format for systematic information. Systematic Biology 46 : 590-621 .
6. MLLER , K. 2006. Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evo lution 38 : 667-676 .
7. RONQUIST , F. , M. TESLENKO , P. VAN DER MARK , D. L. AYRES , A. DARLING , S. HHNA , B. LARGET , ET AL . 2012 . MrBayes 3.2: Eff icient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61 : 539-542 .
8. SIMMONS , M. P. , AND H. OCHOTERENA . 2000 . Gaps as characters in sequence-based phylogenetic analysis. Systematic Biology 49 : 369-381 .
9. STAMATAKIS , A. 2006 . RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22 : 2688-2690 .
10. YOUNG , N. D. , AND J. HEALY . 2003 . GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinformatics 4 : 6 .
11. ZWICKL , D. J. 2006 . Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD dissertation, The University of Texas at Austin, Austin, Texas, USA.